...

1. Become comfortable with the basic steps of indexing a reference genome, mapping reads, and converting output to SAM/BAM format for downstream analysis.
2. Use bowtie2 to map reads from an E. coli Illumina data set to a reference genome and compare the output.

Theory

Please see the Introduction the Introduction to mapping presentation on presentation on the course outline for more details of the theory behind read mapping algorithms and critical considerations for using these tools and references correctly.

...